Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Satb1

Cell type

Cell type Class
Neural
Cell type
Brain
MeSH Description
The part of CENTRAL NERVOUS SYSTEM that is contained within the skull (CRANIUM). Arising from the NEURAL TUBE, the embryonic brain is comprised of three major parts including PROSENCEPHALON (the forebrain); MESENCEPHALON (the midbrain); and RHOMBENCEPHALON (the hindbrain). The developed brain consists of CEREBRUM; CEREBELLUM; and other structures in the BRAIN STEM.

Attributes by original data submitter

Sample

source_name
SATB1 Wild-type
cell type
Brain
age
5 weeks
strain
C57BL/6
antibody
Satb1 1583D
chip antibody vendor
home made
genotype
SATB1 Wild-type
chromatin
urea purified chromatin

Sequenced DNA Library

library_name
GSM5740048
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
chromatin preparation for urea ChIPseq experiment: The protocol for urea ChIP-seq is briefly described. Single cell suspension prepared from tissues were cross-linked with 1% formaldehyde for 10 min at room temperature. After quenching cross-linking reaction (0.125M Gly at final), these cells were lysed in buffer (4% SDS, 50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 100 mM NaCl) with Protease inhibitor (Roche) and RNase inhibitor and loaded on top of 8 M urea followed by ultracentrifugation in a Beckman TL-100 Ultracentrifuge for 4-5 hrs at 45K rpm (181,000g, g=relative centrifugation force or RCF; TLS55 rotor). Recovered chromatin pellet was sonicated using Branson sonifier (20% power, 10 sec on and 30 sec off for 4-6 cycles) in sonication buffer (0.5% Na-laurylsarcosine, 0.1% DOC, 1mM EDTA, 0.5mM EGTA, 10mM Tris-HCl, 100mM NaCl) with Protease inhibitor and RNase inhibitor. The reverse cross-linking of chromatin aliquot was done at 65°C overnight in buffer containing 1% SDS, 100 mM NaCl, 1 mM EDTA, 10mMTris-HCl. Samples were further treated by 100 µg/ml RNase A at 37°C for 1 hr, 200 µg/ml proteinase K at 60°C for more than 3 hrs, followed by DNA purification. For chromatin-immunoprecipitation, 1 µg of an antibody of choice were added to 10 ~ 20 µg of sonicated solubilized chromatin in 350 µl in dilution buffer (1% Triton X-100, 0.01% SDS, 1 mM EDTA, 15 mM Tris-HCl, 100 mM NaCl) and incubated overnight at 4°C. The chromatin fragments bound to antibodies (after incubation overnight) were captured using 40 µl of protein-A or protein-G Dynabeads (Invitrogen; pre-washed with 0.1% BSA [Fraction V, Sigma), by 4 hrs incubation time. After beads washing and DNA elution from beads, ChIP DNAs was reverse-crosslinked at 65oC overnight, followed by RNase-A treatment and proteinase K treatments as described above. The recovered DNA was further purified with a QIAquick PCR purification kit (Qiagen), with elution in 15µl of Qiagen Elution Buffer (alternatively, Phenol-chloroform extraction and ethanol precipitation). The purified DNAs were subjected to ChIP-seq library construction.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
48167715
Reads aligned (%)
69.1
Duplicates removed (%)
48.7
Number of peaks
57076 (qval < 1E-05)

mm9

Number of total reads
48167715
Reads aligned (%)
69.0
Duplicates removed (%)
48.8
Number of peaks
56909 (qval < 1E-05)

Base call quality data from DBCLS SRA